It is essential that the genome be passed faithfully from parents to their offspring. Threats to faithful genome transmission come from limitations on the fidelity of replication, errors in chromosome segregation, and from the deleterious activity of parasitic genetic elements, transposons, which propagate by increasing their copy numbers in germ cell genomes. The challenge of transposon control is formidable. In Drosophila, more than 200 different elements are distributed among highly divergent families. These elements use different mobilization strategies and share no universal proteins or cofactors. Thus, the host must somehow discriminate this diversity of elements from protein coding genes and selectively silence the former. Over the past 6 years, we have come to understand that the piRNA pathway plays a critical role in reproductive tissues, embodying an essential defense mechanism against mobile genetic elements. Studies, mainly in Drosophila and mice, have established a molecular framework for how the piRNA pathway operates and have implicated a growing list of protein cofactors in its various stages. While we have produced a coarse model for piRNA production and for the mechanisms by which the pathway silences transposons, we are only just beginning to understand many of the molecular events that form the mechanistic basis of this innate immune system Our goal in this proposal is to address three key, outstanding issues. First, we wish to understand how the definition of a transposon is established in the form of a piRNA repertoire. This entails deciphering the regulation of piRNA generative loci, the mechanisms which mark RNAs to be processed into piRNAs, and the mechanics of piRNA biogenesis. Second, we will uncover the biochemistry of target repression by Piwi protein/piRNA complexes at both the transcriptional and post-transcriptional levels. Third, will probe the functions of maternally inherited piRNAs and their roles in germ cells and in the soma. By accomplishing these aims, we will contribute to the understanding of one of the most deeply rooted biological imperatives, the need to conserve the integrity of the germ line!